'''
Created on Sep 21, 2010

@author: oabalbin

1. get set of exons intervals
2. get the sequences from galaxy
3. make the transcriptome
*5. build a bowtie index
4. get the coverage for those positions from the bam files: extract reads from mirDeep2.
7. run the bwa_converter
8. cat the sequences reads.fa
9. cat the sequences .arf
10. chopped the reads
11. run miRDeep2.
'''
